In fact, Japan scored a couple of superb tries through wing Kenki Fukuoka, and only trailed 18-17. However, Scotland's superior strength finally told.
Two Greig Laidlaw penalties gave Scotland an early lead, but the main talking points in the opening stages were Japan's struggles in the scrum and the way the Murrayfield pitch was cutting up.
Good work from the forwards allowed Ruaridh Jackson to put Tommy Seymour over for the first try, before Ayumu Goromaru got Japan off and running with a penalty. 11-3 the score at half time.
The visitors then scored a sensational try as slick handling across the back line saw Fukuoka cross on the left.
Laidlaw scampered over from close range, before Fukuoka struck again, this time finishing after a great run by Goromaru.
An upset was on the cards, but Scotland showed a ruthless streak in the final quarter.
Seymour added his second, former Gloucester prop Alasdair Dickinson finished off some great handling by his team mates and Duncan Weir and Sean Lamont added further tries to complete the scoring.
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